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- PDB-6mkw: Crystal structure of the periplasmic Lysine-, Arginine-, Ornithin... -

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Basic information

Entry
Database: PDB / ID: 6mkw
TitleCrystal structure of the periplasmic Lysine-, Arginine-, Ornithine-binding protein (LAO) D11A mutant from Salmonella typhimurium complexed with histidine
ComponentsLysine/arginine/ornithine transport protein
KeywordsPROTEIN BINDING / Periplasmic Binding Protein / LAO / Thermodynamics / Protein Ligand Complex
Function / homology
Function and homology information


amino acid binding / amino acid transport / outer membrane-bounded periplasmic space
Similarity search - Function
Specific amino acids and opine-binding periplasmic protein, ABC transporter / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HISTIDINE / Lysine/arginine/ornithine transport protein / Lysine/arginine/ornithine-binding periplasmic protein
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsRomero-Romero, S. / Vergara, R. / Espinoza-Perez, G. / Rodriguez-Romero, A.
Funding support Mexico, 4items
OrganizationGrant numberCountry
Other governmentIN208418 Mexico
Other government221169 Mexico
Other government254514 Mexico
Other governmentIN220516 Mexico
CitationJournal: Febs J. / Year: 2020
Title: The interplay of protein-ligand and water-mediated interactions shape affinity and selectivity in the LAO binding protein.
Authors: Vergara, R. / Romero-Romero, S. / Velazquez-Lopez, I. / Espinoza-Perez, G. / Rodriguez-Hernandez, A. / Pulido, N.O. / Sosa-Peinado, A. / Rodriguez-Romero, A. / Fernandez-Velasco, D.A.
History
DepositionSep 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine/arginine/ornithine transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2844
Polymers25,9431
Non-polymers3403
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.897, 59.016, 115.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysine/arginine/ornithine transport protein


Mass: 25943.225 Da / Num. of mol.: 1 / Mutation: D11A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain 14028s / SGSC 2262) (bacteria)
Strain: 14028s / SGSC 2262 / Gene: argT, STM14_2901 / Plasmid: pET12b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: A0A0F6B499, UniProt: P02911*PLUS
#2: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Sodium acetate trihydrate 0.1 M Sodium cacodylate trihydrate 30% w/v Polyethylene glycol 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 10, 2018 / Details: Osmic VariMax Cu-HF
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 11213 / % possible obs: 97.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 19.2 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.098 / Net I/σ(I): 22.1
Reflection shellResolution: 2.32→2.36 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1055 / CC1/2: 0.885 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260:)refinement
HKL-3000Rdata reduction
HKL-3000Rdata scaling
PHENIX(1.14_3260)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LAG

1lag


Resolution: 2.32→35.148 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.56
RfactorNum. reflection% reflection
Rfree0.2284 1000 8.92 %
Rwork0.1731 --
obs0.1781 11207 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.32→35.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 23 119 1928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011886
X-RAY DIFFRACTIONf_angle_d1.0022561
X-RAY DIFFRACTIONf_dihedral_angle_d5.4491519
X-RAY DIFFRACTIONf_chiral_restr0.057284
X-RAY DIFFRACTIONf_plane_restr0.006336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3171-2.43930.24841280.20631316X-RAY DIFFRACTION91
2.4393-2.59210.28531410.20381438X-RAY DIFFRACTION98
2.5921-2.79210.26671430.19781444X-RAY DIFFRACTION98
2.7921-3.07290.25671440.17941475X-RAY DIFFRACTION99
3.0729-3.51730.2341430.1661465X-RAY DIFFRACTION99
3.5173-4.430.1941470.13991493X-RAY DIFFRACTION99
4.43-35.15240.19741540.17411576X-RAY DIFFRACTION98

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